Comprehensive assessment on urban ecological system is one of important issues for regional sustainable development research. Urban eco-efficiency is the effective tool to integrate sustainabable strategies into the development planning and management initiatives, which expresses the relationship of inputs of ecological impact and outputs of social welfare. An evaluation model of urban sustainability based on eco-efficiency was proposed by integrating Ecological Footprint model and Human Development Index. Using this model, a case study of Xiamen City was carried out using the statistical data from 2000 to 2006. There is a fluctuation of ecoefficiency which showed a steady increase first, then a sharp decline and a marginal increase towards the end. During 2000-2006, the per-capita ecological footprint increases from 4.279 hm2 to 5.462 hm2; and the Human Development Index increases from 0.831 to 0.896; thus the eco-efficiency, resource efficiency and environmental efficiency declines by 15.5%, 15.7% and 15.3% respectively. Xiamen experiences sustainability hypo-increasing phase first, sustainability increasing phase secondly, then sustainability decreasing phase, and sustainability increasing phase in the end. On the whole, the urban sustainability shows a decreasing trend.